Molecular-Docking-Guided Design, Synthesis, and Biologic Evaluation of Radioiodinated Quinazolinone Prodrugs

Electrochemical oxidative decarboxylative of α-oxocarboxylic acids towards the synthesis of quinazolines and quinazolinones

A mild and environmentally electrochemical method for the synthesis of quinazolines and quinazolinones has been developed through anodic oxidation decarboxylative of α-oxocarboxylic acids. The present reaction was efficiently conducted by using simple and cheap NH4I as the N-source and electrolyte in an undivided cell. The desired products, quinazolines and quinazolinones, were isolated in high yield under chemical oxidant free conditions.

Electrochemical-Induced C-N Bond Formation: A New Method to Synthesis (Z)-Quinazolinone Oximes Using Primary Amines and Quinazolin-4(3H)-one

A novel and highly selective electrochemical method for the synthesis of diverse quinazolinone oximes via direct electrooxidation of primary amines/C(sp2)-H functionalization of oximes has been developed. The reaction is conducted in an undivided cell under constant current conditions and is oxidant-free, open-air, and eco-friendly. Notably, the protocol shows good functional group tolerance, providing versatile quinazolinone oximes in good yields. Moreover, the mechanism is investigated through control experiments and cyclic voltammogram (CV) experiments.

Tailoring the AIE Chromogen 2-(2-Hydroxyphenyl)benzothiazole for Use in Enzyme-Triggered Molecular Brachytherapy

A targeted strategy for treating cancer is antibody-directed enzyme prodrug therapy, where the enzyme attached to the antibody causes conversion of an inactive small-molecule prodrug into an active drug. A limitation may be the diffusion of the active drug away from the antibody target site. A related strategy with radiotherapeutics entails enzymatically promoted conversion of a soluble to insoluble radiotherapeutic agent, thereby immobilizing the latter at the target site. Such a molecular brachytherapy has been scarcely investigated. In distinct research, the advent of molecular designs for aggregation-induced emission (AIE) suggests translational use in molecular brachytherapy. Here, several 2-(2-hydroxyphenyl)benzothiazole substrates that readily aggregate in aqueous solution (and afford AIE) were elaborated in this regard. In particular, (1) the 2-(2-hydroxyphenyl) unit was derivatized to bear a pegylated phosphodiester that imparts water solubility yet undergoes enzymatic cleavage, and (2) a p-phenol unit was attached to the benzo moiety to provide a reactive site for final-step iodination (here examined with natural abundance iodide). The pegylated phosphodiester-iodinated benzothiazole undergoes conversion from aqueous-soluble to aqueous-insoluble upon treatment with a phosphatase or phosphodiesterase. The aggregation is essential to molecular brachytherapy, whereas the induced emission of AIE is not essential but provides a convenient basis for research development. Altogether, 21 compounds were synthesized (18 new, 3 known via new routes). Taken together, blending biomedical strategies of enzyme prodrug therapy with materials chemistry concerning substances that undergo AIE may comprise a step forward on the long road toward molecular brachytherapy.

Computational Simulations to Guide Enzyme-Mediated Prodrug Activation

Prodrugs are designed to improve pharmaceutical/biopharmaceutical characteristics, pharmacokinetic/pharmacodynamic properties, site-specificity, and more. A crucial step in successful prodrug is its activation, which releases the active parent drug, exerting a therapeutic effect. Prodrug activation can be based on oxidation/reduction processes, or through enzyme-mediated hydrolysis, from oxidoreductases (i.e., Cytochrome P450) to hydrolytic enzymes (i.e., carboxylesterase). This study provides an overview of the novel in silico methods for the optimization of enzyme-mediated prodrug activation. Computational methods simulating enzyme-substrate binding can be simpler like molecular docking, or more complex, such as quantum mechanics (QM), molecular mechanics (MM), and free energy perturbation (FEP) methods such as molecular dynamics (MD). Examples for MD simulations used for elucidating the mechanism of prodrug (losartan, paclitaxel derivatives) metabolism via CYP450 enzyme are presented, as well as an MD simulation for optimizing linker length in phospholipid-based prodrugs. Molecular docking investigating quinazolinone prodrugs as substrates for alkaline phosphatase is also presented, as well as QM and MD simulations used for optimal fit of different prodrugs within the human carboxylesterase 1 catalytical site. Overall, high quality computational simulations may show good agreement with experimental results, and should be used early in the prodrug development process.

Transition metal-free C-F/C-Cl/C-C cleavage of ClCF2COONa for the synthesis of heterocycles

A transition metal-free and external oxidant-free annulation of substrates having two nitrogen-nucleophilic sites with ClCF₂COONa was demonstrated, affording a series of 1,3,5-triazines and quinazolinones in up to 96% yields. Notably, ClCF₂COONa was employed as the C1 synthon for valuable heterocycles. Using this protocol, two C-N bonds were formed in one pot via the cleavage of two C-F bonds, one C-Cl bond and one C-C bond. This method avoided the use of a transition metal and an oxidant and generated low toxicity inorganic waste.

Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy

Subunit vaccines have been investigated in over 1000 clinical trials of cancer immunotherapy, but have shown limited efficacy. Nanovaccines may improve efficacy but have rarely been clinically translated. By conjugating molecular vaccines with Evans blue (EB) into albumin-binding vaccines (AlbiVax), here we develop clinically promising albumin/AlbiVax nanocomplexes that self-assemble in vivo from AlbiVax and endogenous albumin for efficient vaccine delivery and potent cancer immunotherapy. PET pharmacoimaging, super-resolution microscopies, and flow cytometry reveal almost 100-fold more efficient co-delivery of CpG and antigens (Ags) to lymph nodes (LNs) by albumin/AlbiVax than benchmark incomplete Freund's adjuvant (IFA). Albumin/AlbiVax elicits ~10 times more frequent peripheral antigen-specific CD8⁺ cytotoxic T lymphocytes with immune memory than IFA-emulsifying vaccines. Albumin/AlbiVax specifically inhibits progression of established primary or metastatic EG7.OVA, B16F10, and MC38 tumors; combination with anti-PD-1 and/or Abraxane further potentiates immunotherapy and eradicates most MC38 tumors. Albumin/AlbiVax nanocomplexes are thus a robust platform for combination cancer immunotherapy.

Synthesis, Polymorphism, and Insecticidal Activity of Methyl 4-(4-chlorophenyl)-8-iodo-2-methyl-6-oxo-1,6-dihydro-4H-pyrimido[2,1-b]quinazoline-3-Carboxylate Against Anopheles arabiensis Mosquito

Mosquitoes are the major vectors of pathogens and parasites including those causing malaria, the most deadly vector-borne disease. The negative environmental effects of most synthetic compounds combined with widespread development of insecticide resistance encourage an interest in finding and developing alternative products against mosquitoes. In this study, pyrimido[2,1-b]quinazoline derivative DHPM3 has been synthesized by three-step chemical reaction and screened for larvicide, adulticide, and repellent properties against Anopheles arabiensis, one of the dominant vectors of malaria in Africa. The title compound emerged as potential larvicide agent for further research and development, because it exerted 100% mortality, while adulticide activity was considered moderate.

Boramino acid as a marker for amino acid transporters

Amino acid transporters (AATs) are a series of integral channels for uphill cellular uptake of nutrients and neurotransmitters. Abnormal expression of AATs is often associated with cancer, addiction, and multiple mental diseases. Although methods to evaluate in vivo expression of AATs would be highly useful, efforts to develop them have been hampered by a lack of appropriate tracers. We describe a new class of AA mimics-boramino acids (BAAs)-that can serve as general imaging probes for AATs. The structure of a BAA is identical to that of the corresponding natural AA, except for an exotic replacement of the carboxylate with -BF3 (-). Cellular studies demonstrate strong AAT-mediated cell uptake, and animal studies show high tumor-specific accumulation, suggesting that BAAs hold great promise for the development of new imaging probes and smart AAT-targeting drugs.

Copper-catalyzed radical methylation/C-H amination/oxidation cascade for the synthesis of quinazolinones

A copper-catalyzed radical methylation/sp(3) C-H amination/oxidation reaction for the facile synthesis of quinazolinone was developed. In this cascade reaction, dicumyl peroxide acts not only as a useful oxidant but also as an efficient methyl source. Notably, a methyl radical, generated from peroxide, was confirmed by electron paramagnetic resonance for the first time.

Synthesis and Characterisation of Phosphazene Derivatives Containing Dioxybiphenyl and 4-Sulfanylquinazoline Groups

2,2-Dichloro-4,4,6,6-bis[spiro(2′,2″-dioxy-1′,1″-biphenylyl)]cyclotriphosphazene was synthesised from the reaction of hexachlorocyclotriphosphazene with biphenyl-2,2′-diol. 2,2-Bis(4-formylphenoxy)-4,4,6,6-bis[spiro(2′,2″-dioxy-1′,1″-biphenylyl)]cyclotriphosphazene was obtained from the reaction of 2,2-dichloro-4,4,6,6-bis[spiro(2′,2″-dioxy-1′,1″-biphenylyl)] cyclotriphosphazene with 4-hydroxybenzaldehyde. 2,2-Bis[4-(4-quinazolinone)phenoxy]-4,4,6,6-bis[spiro(2′,2″-dioxy-1′,1″-biphenylyl)]cyclotriphosphazene was synthesised from the reaction of 2,2-bis(4-formylphenoxy)-4,4,6,6-bis[spiro(2′,2″-dioxy-1′,1″-biphenylyl)]cyclotriphosphazene with anthranilamide in N,N-dimethylformamide. The novel cyclophosphazene derivatives were synthesised under mild conditions from the reaction of 2,2-bis[4-(4-quinazolinone)phenoxy]-4,4,6,6-bis[spiro(2′,2″-dioxy-1′,1″-biphenylyl)]cyclotriphosphazene with 4-chlorobenzenemethanethiol, p-thiocresol, 4-aminothiophenol, and 4-chlorothiophenol in the presence of p-toluenesulfonyl chloride via C-OH bond activation under mild conditions. All products were generally obtained in high yields. Their structures were characterised by HRMS, IR and 1H, 13C spectroscopy.

6',7'-Dimeth-oxy-1',2'-dihydro-spiro-[cyclo-hexane-1,2'-quinazolin]-4'(3'H)-one

In the title compound, C(15)H(20)N(2)O(3), prepared from the reaction of 2-amino-4,5-dimeth-oxy-benzonitrile and cyclo-hexa-none, the six-membered diaza ring assumes an envelope conformation. In the crystal, inversion dimers are formed by pairs of N-H⋯O hydrogen bonds. Futher N-H⋯O hydrogen bonds link the dimers into a two-dimensional structure parallel to (001).

Human placental alkaline phosphatase-mediated hydrolysis correlates tightly with the electrostatic contribution from tail group

Human placental alkaline phosphatase has been identified as a hydrolase that is significantly overexpressed on the surface of various solid tumor cells, and is therefore a suitable prodrug design target for non-invasive cancer imaging and therapy. Structure-based prediction of enzymatic activities is essential for rational prodrug design. We have been probing the catalytic proficiency--(k(cat) /K(M) )/k(w)--of placental alkaline phosphatase toward several widely diverse substrate structures experimentally and correlating these results to in silico predictions that are based on the free energy estimates obtained from docking of each substrate structure with placental alkaline phosphatase. We have found that electrostatic contribution from the tail group is the most crucial factor to determine the catalytic efficiencies of the substrates. The electrostatic contribution and the total binding energy of the tail group are well correlated with catalytic efficiencies (R² = 0.79 and 0.89, respectively). However, hydrophobic contribution from the tail group does not correlate with the catalytic efficiencies (negative correlation, R² = 0.27). This supports the prior hypothesis stating that alkaline phosphatase-mediated differential hydrolysis of its substrates is attributable to the differential interactions with the tail group, determined by the electrostatic contributions from the non-bridging oxygen atoms. Calculation of the electrostatic potentials within the active site of human placental alkaline phosphatase also suggests that the local positive electrostatic environment may account for its capability to distinguish various substrates. Our study is likely to have immediate implications in the design of prodrugs against human placental alkaline phosphatase and other esterases overexpressed by human tumor cells.

Using molecular docking to investigate the anti-breast cancer activity of low molecular weight compounds present on wild mushrooms

Mushrooms represent an unlimited source of compounds with anti-tumour and immunostimulating properties, and their intake has been shown to reduce the risk of breast cancer. A large number of low molecular weight (LMW) compounds present in mushrooms have been identified, including phenolic acids, flavonoids, tocopherols, carotenoids, sugars and fatty acids. In order to evaluate which wild mushroom LMW compounds may be involved in anti-breast cancer activity we selected a representative dataset of 43 LMW compounds and performed molecular docking against three known protein targets involved in breast cancer (aromatase, estrone sulfatase and 17β-HSD-1) using AutoDock4 as docking software. The estimated inhibition constants for all LMW compounds were determined, and the potential structure-activity relationships for the compounds with the best estimated inhibition constants are discussed for each compound family. 4-O-caffeoylquinic, naringin and lycopene stand out as the top-ranked potential inhibitors for aromatase, estrone sulfatase and 17β-HSD1, respectively, and the 3-D docked conformations for these compounds are discussed in detail. This information provides several interesting starting points for further development of aromatase, estrone sulfatase and 17β-HSD1 inhibitors.

Integrated bioinformatics analysis for cancer target identification

The exponential growth of high-throughput Omics data has provided an unprecedented opportunity for new target identification to fuel the dried-up drug discovery pipeline. However, the bioinformatics analysis of large amount and heterogeneous Omics data has posed a great deal of technical challenges for experimentalists who lack statistical skills. Moreover, due to the complexity of human diseases, it is essential to analyze the Omics data in the context of molecular networks to detect meaningful biological targets and understand disease processes. Here, we describe an integrated bioinformatics analysis strategy and provide a running example to identify suitable targets for our in-house Enzyme-Mediated Cancer Imaging and Therapy (EMCIT) technology. In addition, we go through a few key concepts in the process, including corrected false discovery rate (FDR), Gene Ontology (GO), pathway analysis, and tissue specificity. We also describe popular programs and databases which allow the convenient annotation and network analysis of Omics data. We provide a practical guideline for researchers to quickly follow the protocol described and identify those targets that are pertinent to their work.

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters

Background

Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters.

Implementation

MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections.

Conclusion

MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.

Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping

Solution-state nuclear magnetic resonance (NMR) is a versatile tool for the study of binding interactions between small molecules and macromolecular targets. We applied ligand-based NMR techniques to the study of human thymidylate synthase (hTS) using known nanomolar inhibitors and a library of small molecule fragments. Screening by NMR led to the rapid identification of ligand pairs that bind in proximal sites within the cofactor-binding pocket of hTS. Screening hits were used as search criteria within commercially available sources, and a subset of catalog analogs were tested for potency by in vitro assay and binding affinity by quantitative saturation transfer difference (STD)-NMR titration. Two compounds identified by this approach possess low micromolar affinity and potency, as well as excellent binding efficiency against hTS. Relative binding orientations for both leads were modeled using AutoDock, and the most likely bound conformations were validated using experimentally derived STD-NMR binding epitope data. These ligands represent novel starting points for fragment-based drug design of non-canonical TS inhibitors, and their binding epitopes highlight important and previously unexploited interactions with conserved residues in the cofactor-binding site.

Novel prodrugs for targeting diagnostic and therapeutic radionuclides to solid tumors

Most cancer therapeutics (chemo, radiation, antibody-based, anti-angiogenic) are at best partially and/or temporarily effective. In general, the causes for failure can be summarized as: (i) poor diffusion and/or nonuniform distribution of drug/prodrug molecules in solid tumors; (ii) high drug concentration and retention in normal tissues (leading to side effects); (iii) requirement for plasma-membrane permeability and/or internalization of drug/prodrug molecules; (iv) low uptake of drug by tumor; (v) lack of retention of drug within tumor (most have gradient-driven reversible binding); and (vi) multidrug resistance. We are developing an innovative technology that aims to surmount these problems by actively concentrating and permanently entrapping radioimaging and radiotherapeutic prodrugs specifically within solid tumors. The approach will enable noninvasive sensing (imaging) and effective therapy of solid tumors, allowing tumor detection, diagnosis, and treatment to be closely coupled (personalized medicine).

(S)-2-(3-Nitro-phen-yl)-1,2-dihydro-quinazolin-4(3H)-one

In the racemic title compound, C₁₄H₁₁N₃O₃, the pyrimidine ring has an envelope conformation with the puckering parameters Q = 0.3338 (17) Å, Θ = 60.1 (3) and ϕ = 290.4 (3)°. The two N—H groups form hydrogen bonds with symmetry-related mol­ecules, building a two-dimensional network parallel to the (10) plane.

DMSO increases radioiodination yield of radiopharmaceuticals

A high-yield radioiodination method for various types of molecules is described. The approach employs DMSO as precursor solvent, a reaction ratio of 2-5 precursor molecules per iodine atom, 5-10 microg oxidant, and a 10-25 microl reaction volume. The solution is vortexed at room temperature for 1-5 min and progress of the reaction is assessed by HPLC. Radioiodinated products are obtained in > or = 95% yield and meet the requirements for radiotracer imaging, biodistribution studies, and molecular and cellular biology research.

Computational Modeling and Experimental Evaluation of a Novel Prodrug for Targeting the Extracellular Space of Prostate Tumors

We are developing a noninvasive approach for targeting imaging and therapeutic radionuclides to prostate cancer. Our method, Enzyme-Mediated Cancer Imaging and Therapy (EMCIT), aims to use enzyme-dependent, site-specific, in vivo precipitation of a radioactive molecule within the extracellular space of solid tumors. Advanced methods for data mining of the literature, protein databases, and knowledge bases (IT. Omics LSGraph and Ingenuity Systems) identified prostatic acid phosphatase (PAP) as an enzyme overexpressed in prostate cancer and secreted in the extracellular space. Using AutoDock 3.0 software, the prodrug ammonium 2-(2'-phosphoryloxyphenyl)-6-iodo-4-(3H)-quinazolinone (IQ(2-P)) was docked in silico into the X-ray structure of PAP. The data indicate that IQ(2-P) docked into the PAP active site with a calculated inhibition constant (K(i)) more favorable than that of the PAP inhibitor alpha-benzylaminobenzylphosphonic acid. When (125)IQ(2-P), the radioiodinated form of the water-soluble prodrug, was incubated with PAP, rapid hydrolysis of the compound was observed as exemplified by formation of the water-insoluble 2-(2'-hydroxyphenyl)-6-[(125)I]iodo-4-(3H)-quinazolinone ((125)IQ(2-OH)). Similarly, the incubation of IQ(2-P) with human LNCaP, PC-3, and 22Rv1 prostate tumor cells resulted in the formation of large fluorescent IQ(2-OH) crystals. No hydrolysis was seen in the presence of normal human cells. Autoradiography of tumor cells incubated with (125)IQ(2-P) showed accumulation of radioactive grains ((125)IQ(2-OH)) around the cells. We anticipate that the EMCIT approach will enable the active in vivo entrapment of radioimaging and radiotherapeutic compounds within the extracellular spaces of primary prostate tumors and their metastases.